**5. Conclusions**

In conclusion, the number of cultured non-*Helicobacter* bacteria decreased in the washed biopsies, suggesting that they might be a transient contamination from oral cavity; however, in the microbiome analysis, no significant differences in the bacterial diversity were observed between unwashed and

washed biopsies. The bacterial diversity in biopsies that were *H. pylori*-positive and *H. pylori*-negative was significantly different, implying that *H. pylori* is the major modulator of gastric microbiome. Further large-scale studies are required to investigate the transient and persistent gastric microbiota. This may include an increased number of samples, investigation of dysbiosis, a wider range of culture conditions and growth media, metatranscriptomic analysis, immunological assays or additional treatment of biopsies.

**Author Contributions:** Conceptualization, J.K., L.K. and L.P.A.; methodology, J.K., L.K. and L.P.A.; validation, M.R.S., T.B.J., T.H.F., K.F. and L.P.A.; formal analysis, M.R.S., T.B.J. and K.F.; investigation, M.R.S., M.U., J.S. and L.J.; resources, J.K., J.S., K.F. and L.P.A.; data curation, M.R.S., T.B.J. and M.U.; writing—original draft preparation, M.R.S.; writing—review and editing, M.R.S., J.K. and L.P.A.; visualization, M.R.S., T.B.J. and K.F.; supervision, J.K., K.F., L.K. and L.P.A.; project administration, J.K.; funding acquisition, J.K. and L.K. All authors have read and agreed to the published version of the manuscript.

**Funding:** The collection and processing of samples in Lithuania was funded by Lithuanian Research Council under the gran<sup>t</sup> No. APP-2/2016.

**Acknowledgments:** The authors would like to acknowledge Justina Arstikyte for excellent work in the lab.

**Conflicts of Interest:** The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses or interpretation of data; in the writing of the manuscript or in the decision to publish the results.
